RNA-seq analysis forVishal group at Longwood.
Contact Lorena Pantano (lpantano@hsph.harvard.edu) for additional details.
The most recent update of this html document occurred: Mon May 23 17:31:32 2016
The sections below provide code to reproduce the included results and plots.
2016-05-23 16:47:20 INFO::Using gene counts calculated from the Sailfish transcript counts.
Trimmed mean of M-values (TMM) normalization is described here
Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3). doi:10.1186/gb-2010-11-3-r25
We used RUVSeq package for this with two factors to explain the unwanted variation.
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004075
out of 29943 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 3185, 11%
LFC < 0 (down) : 3326, 11%
outliers [1] : 468, 1.6%
low counts [2] : 7996, 27%
(mean count < 2)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results
NULL
Differential expression file at: fa_model.tsv
Normalized counts matrix file at: fa_model_log2_counts.tsv
Plot top 9 genes
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | symbol | description | day14vscontrol | day1vscontrol | day2vscontrol | day3vscontrol | day7vscontrol | absMaxLog2FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSMUSG00000040405 | 16311.0902 | 1.2719380 | 0.3326644 | 477.9036 | 0 | 0 | Havcr1 | hepatitis A virus cellular receptor 1 | 1.2719380 | 6.9619885 | 5.793616 | 4.7710459 | 3.4953820 | 6.961989 |
| ENSMUSG00000028017 | 2685.7105 | -0.7611039 | 0.4579820 | 285.1583 | 0 | 0 | Egf | epidermal growth factor | -0.7611039 | -6.4691406 | -7.250125 | -3.7313804 | -2.3649677 | 7.250125 |
| ENSMUSG00000034810 | 113.2406 | 2.0116777 | 0.3500331 | 229.7995 | 0 | 0 | Scn7a | sodium channel, voltage-gated, type VII, alpha | 2.0116777 | -2.3141228 | -3.457986 | 0.2384421 | 1.3554646 | 3.457986 |
| ENSMUSG00000027199 | 5005.4187 | -1.5908413 | 0.4126514 | 220.4895 | 0 | 0 | Gatm | glycine amidinotransferase (L-arginine:glycine amidinotransferase) | -1.5908413 | -5.2620713 | -4.538672 | -3.5990810 | -2.8571068 | 5.262071 |
| ENSMUSG00000026348 | 765.4457 | -1.4919020 | 0.2984488 | 214.3869 | 0 | 0 | Acmsd | amino carboxymuconate semialdehyde decarboxylase | -1.4919020 | -4.0416947 | -2.666851 | -2.6443023 | -2.2875425 | 4.041695 |
| ENSMUSG00000022037 | 8324.4031 | 2.2479713 | 0.3298258 | 210.9215 | 0 | 0 | Clu | clusterin | 2.2479713 | 3.9511690 | 5.004188 | 4.2887266 | 3.2508579 | 5.004188 |
| ENSMUSG00000029304 | 219108.8212 | 3.3383981 | 0.4638694 | 203.0990 | 0 | 0 | Spp1 | secreted phosphoprotein 1 | 3.3383981 | 6.8407038 | 7.447928 | 5.9425678 | 5.1756161 | 7.447928 |
| ENSMUSG00000041052 | 2823.5800 | -1.0698716 | 0.4527684 | 198.4246 | 0 | 0 | Slc7a13 | solute carrier family 7, (cationic amino acid transporter, y+ system) member 13 | -1.0698716 | -5.1809340 | -5.105784 | -3.1397970 | -3.2483012 | 5.180934 |
| ENSMUSG00000021490 | 10003.5172 | -0.8005353 | 0.3195153 | 196.5071 | 0 | 0 | Slc34a1 | solute carrier family 34 (sodium phosphate), member 1 | -0.8005353 | -4.1142246 | -3.237309 | -1.7122298 | -1.8162714 | 4.114225 |
| ENSMUSG00000021477 | 5669.9734 | 0.9868310 | 0.2445081 | 195.7993 | 0 | 0 | Ctsl | cathepsin L | 0.9868310 | 3.0552194 | 2.494315 | 2.0127698 | 1.1257107 | 3.055219 |
| ENSMUSG00000039997 | 716.2957 | 0.0861251 | 0.2558293 | 182.6815 | 0 | 0 | Ifi203 | interferon activated gene 203 | 0.0861251 | -2.3753208 | -2.284695 | -0.5596117 | 0.3729947 | 2.375321 |
| ENSMUSG00000036594 | 1764.9060 | 2.4493882 | 0.3789872 | 180.5537 | 0 | 0 | H2-Aa | histocompatibility 2, class II antigen A, alpha | 2.4493882 | -1.5734717 | -1.127157 | 1.3145226 | 2.4167275 | 2.449388 |
| ENSMUSG00000083863 | 183.8333 | -2.8207520 | 0.3095867 | 178.8778 | 0 | 0 | NA | NA | -2.8207520 | -2.1878619 | -2.097094 | -3.3755878 | -2.5682524 | 3.375588 |
| ENSMUSG00000004730 | 110.4004 | 2.8857456 | 0.5022537 | 178.3086 | 0 | 0 | Adgre1 | adhesion G protein-coupled receptor E1 | 2.8857456 | -1.3894795 | -2.255088 | 2.0880200 | 3.7236469 | 3.723647 |
| ENSMUSG00000061947 | 379.7477 | 4.2422088 | 0.5163896 | 178.0911 | 0 | 0 | Serpina10 | serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10 | 4.2422088 | 6.3882789 | 6.370973 | 6.3176621 | 5.5438450 | 6.388279 |
| ENSMUSG00000026365 | 3081.0764 | 2.0580137 | 0.3629814 | 176.1463 | 0 | 0 | Cfh | complement component factor h | 2.0580137 | -1.3936267 | -1.926189 | -0.1759390 | 1.6148495 | 2.058014 |
| ENSMUSG00000022445 | 268.3951 | -0.9733166 | 0.4565228 | 175.7693 | 0 | 0 | Cyp2d26 | cytochrome P450, family 2, subfamily d, polypeptide 26 | -0.9733166 | -5.2160295 | -5.364363 | -3.0398488 | -1.7129063 | 5.364363 |
| ENSMUSG00000027962 | 1669.8257 | 5.3771941 | 0.4724509 | 171.2956 | 0 | 0 | Vcam1 | vascular cell adhesion molecule 1 | 5.3771941 | 3.9804218 | 5.191675 | 7.0552413 | 6.0363334 | 7.055241 |
| ENSMUSG00000083563 | 949.2445 | -2.8970301 | 0.3312405 | 168.1643 | 0 | 0 | NA | NA | -2.8970301 | -2.4546197 | -2.361608 | -3.3401756 | -2.7664567 | 3.340176 |
| ENSMUSG00000038608 | 486.6631 | 3.1258137 | 0.3777503 | 166.7087 | 0 | 0 | Dock10 | dedicator of cytokinesis 10 | 3.1258137 | 0.1452071 | 1.155319 | 3.4243127 | 3.4959390 | 3.495939 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0030593 | GO:0030593 | neutrophil chemotaxis | 22/790 | 81/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0097529 | GO:0097529 | myeloid leukocyte migration | 29/790 | 152/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002685 | GO:0002685 | regulation of leukocyte migration | 28/790 | 155/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0050920 | GO:0050920 | regulation of chemotaxis | 27/790 | 181/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0050729 | GO:0050729 | positive regulation of inflammatory response | 20/790 | 109/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:0022409 | GO:0022409 | positive regulation of cell-cell adhesion | 27/790 | 201/23276 | 0.0000000 | 0.0000002 | 0.0000001 |
| GO:1903036 | GO:1903036 | positive regulation of response to wounding | 23/790 | 158/23276 | 0.0000000 | 0.0000004 | 0.0000003 |
| GO:0002696 | GO:0002696 | positive regulation of leukocyte activation | 30/790 | 278/23276 | 0.0000000 | 0.0000021 | 0.0000016 |
| GO:0002526 | GO:0002526 | acute inflammatory response | 18/790 | 111/23276 | 0.0000000 | 0.0000026 | 0.0000020 |
| GO:0070372 | GO:0070372 | regulation of ERK1 and ERK2 cascade | 27/790 | 239/23276 | 0.0000001 | 0.0000035 | 0.0000027 |
| GO:0050863 | GO:0050863 | regulation of T cell activation | 28/790 | 257/23276 | 0.0000001 | 0.0000042 | 0.0000031 |
| GO:0071347 | GO:0071347 | cellular response to interleukin-1 | 13/790 | 61/23276 | 0.0000001 | 0.0000067 | 0.0000050 |
| GO:1902042 | GO:1902042 | negative regulation of extrinsic apoptotic signaling pathway via death domain receptors | 9/790 | 26/23276 | 0.0000001 | 0.0000067 | 0.0000050 |
| GO:0006959 | GO:0006959 | humoral immune response | 22/790 | 175/23276 | 0.0000001 | 0.0000080 | 0.0000060 |
| GO:0045765 | GO:0045765 | regulation of angiogenesis | 25/790 | 221/23276 | 0.0000002 | 0.0000090 | 0.0000067 |
| GO:0070661 | GO:0070661 | leukocyte proliferation | 30/790 | 301/23276 | 0.0000002 | 0.0000090 | 0.0000067 |
| GO:0007162 | GO:0007162 | negative regulation of cell adhesion | 25/790 | 230/23276 | 0.0000003 | 0.0000177 | 0.0000132 |
| GO:0032963 | GO:0032963 | collagen metabolic process | 14/790 | 78/23276 | 0.0000003 | 0.0000177 | 0.0000132 |
| GO:0019221 | GO:0019221 | cytokine-mediated signaling pathway | 30/790 | 314/23276 | 0.0000004 | 0.0000203 | 0.0000152 |
| GO:0002460 | GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 26/790 | 252/23276 | 0.0000005 | 0.0000272 | 0.0000204 |
| GO:0002274 | GO:0002274 | myeloid leukocyte activation | 20/790 | 162/23276 | 0.0000007 | 0.0000332 | 0.0000249 |
| GO:0007596 | GO:0007596 | blood coagulation | 20/790 | 173/23276 | 0.0000019 | 0.0000845 | 0.0000633 |
| GO:0097191 | GO:0097191 | extrinsic apoptotic signaling pathway | 23/790 | 228/23276 | 0.0000035 | 0.0001426 | 0.0001069 |
| GO:0032102 | GO:0032102 | negative regulation of response to external stimulus | 26/790 | 280/23276 | 0.0000038 | 0.0001518 | 0.0001138 |
| GO:0031639 | GO:0031639 | plasminogen activation | 7/790 | 21/23276 | 0.0000039 | 0.0001518 | 0.0001138 |
| GO:0015711 | GO:0015711 | organic anion transport | 30/790 | 354/23276 | 0.0000046 | 0.0001770 | 0.0001326 |
| GO:0045807 | GO:0045807 | positive regulation of endocytosis | 16/790 | 128/23276 | 0.0000072 | 0.0002676 | 0.0002006 |
| GO:0016053 | GO:0016053 | organic acid biosynthetic process | 24/790 | 256/23276 | 0.0000076 | 0.0002784 | 0.0002087 |
| GO:0071346 | GO:0071346 | cellular response to interferon-gamma | 11/790 | 63/23276 | 0.0000079 | 0.0002838 | 0.0002127 |
| GO:0050679 | GO:0050679 | positive regulation of epithelial cell proliferation | 18/790 | 161/23276 | 0.0000096 | 0.0003378 | 0.0002532 |
| GO:0030198 | GO:0030198 | extracellular matrix organization | 21/790 | 210/23276 | 0.0000105 | 0.0003633 | 0.0002724 |
| GO:0034113 | GO:0034113 | heterotypic cell-cell adhesion | 9/790 | 43/23276 | 0.0000114 | 0.0003908 | 0.0002930 |
| GO:0050678 | GO:0050678 | regulation of epithelial cell proliferation | 26/790 | 301/23276 | 0.0000140 | 0.0004648 | 0.0003484 |
| GO:0010810 | GO:0010810 | regulation of cell-substrate adhesion | 18/790 | 167/23276 | 0.0000160 | 0.0005220 | 0.0003913 |
| GO:0002224 | GO:0002224 | toll-like receptor signaling pathway | 12/790 | 82/23276 | 0.0000201 | 0.0006338 | 0.0004751 |
| GO:0042063 | GO:0042063 | gliogenesis | 23/790 | 259/23276 | 0.0000280 | 0.0008432 | 0.0006321 |
| GO:0050708 | GO:0050708 | regulation of protein secretion | 30/790 | 391/23276 | 0.0000313 | 0.0009257 | 0.0006939 |
| GO:0045840 | GO:0045840 | positive regulation of mitotic nuclear division | 9/790 | 53/23276 | 0.0000663 | 0.0016713 | 0.0012528 |
| GO:0050878 | GO:0050878 | regulation of body fluid levels | 25/790 | 311/23276 | 0.0000667 | 0.0016723 | 0.0012536 |
| GO:0030336 | GO:0030336 | negative regulation of cell migration | 19/790 | 203/23276 | 0.0000674 | 0.0016794 | 0.0012589 |
| GO:0019886 | GO:0019886 | antigen processing and presentation of exogenous peptide antigen via MHC class II | 5/790 | 14/23276 | 0.0000690 | 0.0016944 | 0.0012701 |
| GO:0060740 | GO:0060740 | prostate gland epithelium morphogenesis | 7/790 | 33/23276 | 0.0000998 | 0.0022718 | 0.0017030 |
| GO:0007067 | GO:0007067 | mitotic nuclear division | 29/790 | 399/23276 | 0.0001101 | 0.0024721 | 0.0018531 |
| GO:0044275 | GO:0044275 | cellular carbohydrate catabolic process | 9/790 | 58/23276 | 0.0001370 | 0.0027981 | 0.0020975 |
| GO:0048771 | GO:0048771 | tissue remodeling | 16/790 | 163/23276 | 0.0001426 | 0.0028587 | 0.0021429 |
| GO:0009072 | GO:0009072 | aromatic amino acid family metabolic process | 6/790 | 25/23276 | 0.0001528 | 0.0030176 | 0.0022620 |
| GO:0016485 | GO:0016485 | protein processing | 22/790 | 275/23276 | 0.0001915 | 0.0036200 | 0.0027136 |
| GO:0035239 | GO:0035239 | tube morphogenesis | 28/790 | 393/23276 | 0.0002001 | 0.0037178 | 0.0027869 |
| GO:0010038 | GO:0010038 | response to metal ion | 18/790 | 204/23276 | 0.0002181 | 0.0039848 | 0.0029871 |
| GO:0045786 | GO:0045786 | negative regulation of cell cycle | 26/790 | 359/23276 | 0.0002588 | 0.0046292 | 0.0034701 |
| GO:1901605 | GO:1901605 | alpha-amino acid metabolic process | 18/790 | 211/23276 | 0.0003299 | 0.0057347 | 0.0042988 |
| GO:0090068 | GO:0090068 | positive regulation of cell cycle process | 17/790 | 199/23276 | 0.0004701 | 0.0074424 | 0.0055789 |
| GO:0009914 | GO:0009914 | hormone transport | 24/790 | 333/23276 | 0.0004713 | 0.0074424 | 0.0055789 |
| GO:0071900 | GO:0071900 | regulation of protein serine/threonine kinase activity | 27/790 | 394/23276 | 0.0004745 | 0.0074660 | 0.0055966 |
| GO:0010466 | GO:0010466 | negative regulation of peptidase activity | 18/790 | 220/23276 | 0.0005443 | 0.0083202 | 0.0062369 |
| GO:0002697 | GO:0002697 | regulation of immune effector process | 27/790 | 398/23276 | 0.0005540 | 0.0084387 | 0.0063258 |
| GO:0000768 | GO:0000768 | syncytium formation by plasma membrane fusion | 8/790 | 56/23276 | 0.0005711 | 0.0085820 | 0.0064332 |
| GO:0042742 | GO:0042742 | defense response to bacterium | 20/790 | 262/23276 | 0.0006678 | 0.0096927 | 0.0072658 |
| GO:0006875 | GO:0006875 | cellular metal ion homeostasis | 29/790 | 445/23276 | 0.0006703 | 0.0096976 | 0.0072694 |
We used diana function inside cluster R package to separate genes using the expression correlation with time. Clusters with more than 20 genes are shown. A GO and KEGG enrichment is done for each group.
A summary of diana function is copied here:
The diana-algorithm constructs a hierarchy of clusterings, starting with one large cluster containing all n observations. Clusters are divided until each cluster contains only a single observation.
At each stage, the cluster with the largest diameter is selected. (The diameter of a cluster is the largest dissimilarity between any two of its observations.)
To divide the selected cluster, the algorithm first looks for its most disparate observation (i.e., which has the largest average dissimilarity to the other observations of the selected cluster). This observation initiates the "splinter group". In subsequent steps, the algorithm reassigns observations that are closer to the "splinter group" than to the "old party". The result is a division of the selected cluster into two new clusters.
Working with 1024 genes.
Working with 1024 genes
Working with 1024 genes.
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu04110 | mmu04110 | NA | 8/48 | 128/6698 | 2.8e-06 | 0.0002128 | 0.0002031 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:1902042 | GO:1902042 | negative regulation of extrinsic apoptotic signaling pathway via death domain receptors | 6/118 | 26/23276 | 0.0000000 | 0.0000066 | 0.0000053 |
| GO:0097191 | GO:0097191 | extrinsic apoptotic signaling pathway | 11/118 | 228/23276 | 0.0000000 | 0.0000250 | 0.0000200 |
| GO:2001233 | GO:2001233 | regulation of apoptotic signaling pathway | 13/118 | 370/23276 | 0.0000001 | 0.0000362 | 0.0000290 |
| GO:1903034 | GO:1903034 | regulation of response to wounding | 13/118 | 394/23276 | 0.0000001 | 0.0000411 | 0.0000329 |
| GO:0001525 | GO:0001525 | angiogenesis | 12/118 | 424/23276 | 0.0000017 | 0.0004483 | 0.0003584 |
| GO:0006270 | GO:0006270 | DNA replication initiation | 4/118 | 25/23276 | 0.0000073 | 0.0012032 | 0.0009618 |
| GO:0016485 | GO:0016485 | protein processing | 9/118 | 275/23276 | 0.0000114 | 0.0015990 | 0.0012782 |
| GO:0052547 | GO:0052547 | regulation of peptidase activity | 10/118 | 352/23276 | 0.0000126 | 0.0016550 | 0.0013230 |
| GO:0008630 | GO:0008630 | intrinsic apoptotic signaling pathway in response to DNA damage | 6/118 | 105/23276 | 0.0000160 | 0.0019626 | 0.0015689 |
| GO:1903532 | GO:1903532 | positive regulation of secretion by cell | 10/118 | 389/23276 | 0.0000297 | 0.0028315 | 0.0022635 |
| GO:0045786 | GO:0045786 | negative regulation of cell cycle | 9/118 | 359/23276 | 0.0000913 | 0.0063758 | 0.0050968 |
| GO:0031589 | GO:0031589 | cell-substrate adhesion | 8/118 | 284/23276 | 0.0001022 | 0.0066892 | 0.0053473 |
| GO:0042310 | GO:0042310 | vasoconstriction | 5/118 | 93/23276 | 0.0001120 | 0.0071089 | 0.0056828 |
| GO:0010564 | GO:0010564 | regulation of cell cycle process | 10/118 | 467/23276 | 0.0001356 | 0.0083564 | 0.0066801 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu00380 | mmu00380 | NA | 5/59 | 45/6698 | 0.0000416 | 0.0032068 | 0.0028934 |
| mmu04146 | mmu04146 | NA | 5/59 | 80/6698 | 0.0006478 | 0.0249400 | 0.0225022 |
| mmu00330 | mmu00330 | NA | 4/59 | 54/6698 | 0.0012369 | 0.0317478 | 0.0286446 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:1901605 | GO:1901605 | alpha-amino acid metabolic process | 12/132 | 211/23276 | 0.0000000 | 0.0000030 | 0.0000027 |
| GO:0044282 | GO:0044282 | small molecule catabolic process | 10/132 | 245/23276 | 0.0000014 | 0.0002529 | 0.0002274 |
| GO:0006732 | GO:0006732 | coenzyme metabolic process | 10/132 | 273/23276 | 0.0000037 | 0.0005824 | 0.0005236 |
| GO:1990267 | GO:1990267 | response to transition metal nanoparticle | 6/132 | 78/23276 | 0.0000055 | 0.0007606 | 0.0006839 |
| GO:0044283 | GO:0044283 | small molecule biosynthetic process | 12/132 | 448/23276 | 0.0000097 | 0.0010140 | 0.0009118 |
| GO:0019369 | GO:0019369 | arachidonic acid metabolic process | 5/132 | 63/23276 | 0.0000294 | 0.0024557 | 0.0022080 |
| GO:0009308 | GO:0009308 | amine metabolic process | 6/132 | 124/23276 | 0.0000767 | 0.0044173 | 0.0039717 |
| GO:0046128 | GO:0046128 | purine ribonucleoside metabolic process | 8/132 | 255/23276 | 0.0001064 | 0.0053398 | 0.0048012 |
| GO:0044262 | GO:0044262 | cellular carbohydrate metabolic process | 8/132 | 263/23276 | 0.0001316 | 0.0061168 | 0.0054998 |
| GO:0042537 | GO:0042537 | benzene-containing compound metabolic process | 3/132 | 20/23276 | 0.0001894 | 0.0074307 | 0.0066812 |
| GO:0005976 | GO:0005976 | polysaccharide metabolic process | 5/132 | 96/23276 | 0.0002198 | 0.0081145 | 0.0072961 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu05150 | mmu05150 | NA | 5/38 | 51/6698 | 0.0000087 | 0.0006697 | 0.0005493 |
| mmu04145 | mmu04145 | NA | 6/38 | 179/6698 | 0.0004540 | 0.0149832 | 0.0122897 |
| mmu04650 | mmu04650 | NA | 5/38 | 125/6698 | 0.0006402 | 0.0149832 | 0.0122897 |
| mmu04610 | mmu04610 | NA | 4/38 | 76/6698 | 0.0008435 | 0.0149832 | 0.0122897 |
| mmu05020 | mmu05020 | NA | 3/38 | 35/6698 | 0.0009729 | 0.0149832 | 0.0122897 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0031349 | GO:0031349 | positive regulation of defense response | 12/88 | 271/23276 | 0.0000000 | 0.0000007 | 0.0000005 |
| GO:0030593 | GO:0030593 | neutrophil chemotaxis | 8/88 | 81/23276 | 0.0000000 | 0.0000007 | 0.0000005 |
| GO:0006935 | GO:0006935 | chemotaxis | 14/88 | 491/23276 | 0.0000000 | 0.0000014 | 0.0000010 |
| GO:0050778 | GO:0050778 | positive regulation of immune response | 13/88 | 444/23276 | 0.0000000 | 0.0000018 | 0.0000013 |
| GO:1903034 | GO:1903034 | regulation of response to wounding | 12/88 | 394/23276 | 0.0000000 | 0.0000038 | 0.0000028 |
| GO:0042060 | GO:0042060 | wound healing | 11/88 | 326/23276 | 0.0000000 | 0.0000050 | 0.0000036 |
| GO:0002250 | GO:0002250 | adaptive immune response | 11/88 | 372/23276 | 0.0000002 | 0.0000149 | 0.0000108 |
| GO:0006897 | GO:0006897 | endocytosis | 12/88 | 495/23276 | 0.0000004 | 0.0000314 | 0.0000228 |
| GO:0001819 | GO:0001819 | positive regulation of cytokine production | 10/88 | 357/23276 | 0.0000010 | 0.0000835 | 0.0000607 |
| GO:0002274 | GO:0002274 | myeloid leukocyte activation | 7/88 | 162/23276 | 0.0000027 | 0.0002207 | 0.0001604 |
| GO:0032963 | GO:0032963 | collagen metabolic process | 5/88 | 78/23276 | 0.0000117 | 0.0007128 | 0.0005181 |
| GO:0060840 | GO:0060840 | artery development | 5/88 | 88/23276 | 0.0000211 | 0.0010953 | 0.0007961 |
| GO:0050829 | GO:0050829 | defense response to Gram-negative bacterium | 4/88 | 47/23276 | 0.0000300 | 0.0014197 | 0.0010318 |
| GO:2000147 | GO:2000147 | positive regulation of cell motility | 9/88 | 428/23276 | 0.0000350 | 0.0015858 | 0.0011525 |
| GO:0071345 | GO:0071345 | cellular response to cytokine stimulus | 9/88 | 450/23276 | 0.0000516 | 0.0019815 | 0.0014401 |
| GO:0030198 | GO:0030198 | extracellular matrix organization | 6/88 | 210/23276 | 0.0001471 | 0.0039379 | 0.0028620 |
| GO:0050878 | GO:0050878 | regulation of body fluid levels | 7/88 | 311/23276 | 0.0001789 | 0.0045156 | 0.0032818 |
| GO:0001525 | GO:0001525 | angiogenesis | 8/88 | 424/23276 | 0.0002045 | 0.0049508 | 0.0035981 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu05150 | mmu05150 | NA | 4/26 | 51/6698 | 0.0000394 | 0.0017729 | 0.0010783 |
| mmu04514 | mmu04514 | NA | 5/26 | 154/6698 | 0.0002680 | 0.0043780 | 0.0026626 |
| mmu05323 | mmu05323 | NA | 4/26 | 85/6698 | 0.0002919 | 0.0043780 | 0.0026626 |
| mmu05145 | mmu05145 | NA | 4/26 | 128/6698 | 0.0013730 | 0.0125180 | 0.0076133 |
| mmu04621 | mmu04621 | NA | 3/26 | 58/6698 | 0.0013909 | 0.0125180 | 0.0076133 |
| mmu05140 | mmu05140 | NA | 3/26 | 65/6698 | 0.0019338 | 0.0145038 | 0.0088210 |
| mmu05310 | mmu05310 | NA | 2/26 | 24/6698 | 0.0037948 | 0.0243949 | 0.0148367 |
| mmu04145 | mmu04145 | NA | 4/26 | 179/6698 | 0.0046534 | 0.0261755 | 0.0159196 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0002694 | GO:0002694 | regulation of leukocyte activation | 12/50 | 446/23276 | 0.0000000 | 0.0000002 | 0.0000001 |
| GO:0050900 | GO:0050900 | leukocyte migration | 10/50 | 262/23276 | 0.0000000 | 0.0000002 | 0.0000001 |
| GO:0002253 | GO:0002253 | activation of immune response | 9/50 | 295/23276 | 0.0000000 | 0.0000009 | 0.0000006 |
| GO:0030335 | GO:0030335 | positive regulation of cell migration | 10/50 | 415/23276 | 0.0000000 | 0.0000012 | 0.0000007 |
| GO:0001819 | GO:0001819 | positive regulation of cytokine production | 7/50 | 357/23276 | 0.0000107 | 0.0002724 | 0.0001759 |
| GO:0002274 | GO:0002274 | myeloid leukocyte activation | 5/50 | 162/23276 | 0.0000253 | 0.0005347 | 0.0003453 |
| GO:0043410 | GO:0043410 | positive regulation of MAPK cascade | 7/50 | 434/23276 | 0.0000373 | 0.0007415 | 0.0004788 |
| GO:0008360 | GO:0008360 | regulation of cell shape | 4/50 | 121/23276 | 0.0001330 | 0.0020582 | 0.0013290 |
| GO:0060627 | GO:0060627 | regulation of vesicle-mediated transport | 6/50 | 405/23276 | 0.0002225 | 0.0032549 | 0.0021017 |
| GO:0051085 | GO:0051085 | chaperone mediated protein folding requiring cofactor | 2/50 | 12/23276 | 0.0002944 | 0.0040487 | 0.0026143 |
| GO:0006887 | GO:0006887 | exocytosis | 5/50 | 296/23276 | 0.0004265 | 0.0050837 | 0.0032826 |
| GO:0006874 | GO:0006874 | cellular calcium ion homeostasis | 5/50 | 358/23276 | 0.0010052 | 0.0095076 | 0.0061392 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0043252 | GO:0043252 | sodium-independent organic anion transport | 3/36 | 28/23276 | 1.08e-05 | 0.0050942 | 0.0041872 |
NULL
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu04114 | mmu04114 | NA | 5/28 | 114/6698 | 0.0000940 | 0.0039873 | 0.0032549 |
| mmu04110 | mmu04110 | NA | 5/28 | 128/6698 | 0.0001627 | 0.0039873 | 0.0032549 |
| mmu00330 | mmu00330 | NA | 3/28 | 54/6698 | 0.0014072 | 0.0229850 | 0.0187632 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0002685 | GO:0002685 | regulation of leukocyte migration | 7/79 | 155/23276 | 1.00e-06 | 0.0008678 | 0.0006487 |
| GO:0007067 | GO:0007067 | mitotic nuclear division | 10/79 | 399/23276 | 1.00e-06 | 0.0008678 | 0.0006487 |
| GO:0050900 | GO:0050900 | leukocyte migration | 8/79 | 262/23276 | 3.00e-06 | 0.0014303 | 0.0010692 |
| GO:0007126 | GO:0007126 | meiotic nuclear division | 6/79 | 156/23276 | 1.53e-05 | 0.0031920 | 0.0023861 |
| GO:0000075 | GO:0000075 | cell cycle checkpoint | 6/79 | 165/23276 | 2.10e-05 | 0.0031920 | 0.0023861 |
| GO:0050920 | GO:0050920 | regulation of chemotaxis | 6/79 | 181/23276 | 3.53e-05 | 0.0046279 | 0.0034595 |
| GO:0006935 | GO:0006935 | chemotaxis | 9/79 | 491/23276 | 4.27e-05 | 0.0048599 | 0.0036329 |
| GO:0035239 | GO:0035239 | tube morphogenesis | 8/79 | 393/23276 | 5.64e-05 | 0.0055256 | 0.0041305 |
| GO:0044772 | GO:0044772 | mitotic cell cycle phase transition | 7/79 | 295/23276 | 6.50e-05 | 0.0058725 | 0.0043898 |
| GO:0048732 | GO:0048732 | gland development | 8/79 | 408/23276 | 7.33e-05 | 0.0058725 | 0.0043898 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu04973 | mmu04973 | NA | 2/9 | 39/6698 | 0.0011591 | 0.03825 | 0.0353828 |
NULL
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu05143 | mmu05143 | NA | 2/5 | 32/6698 | 0.0002192 | 0.0013150 | 0.0004614 |
| mmu05144 | mmu05144 | NA | 2/5 | 47/6698 | 0.0004755 | 0.0014266 | 0.0005006 |
| mmu00532 | mmu00532 | NA | 1/5 | 22/6698 | 0.0163201 | 0.0288966 | 0.0101392 |
| mmu00534 | mmu00534 | NA | 1/5 | 26/6698 | 0.0192644 | 0.0288966 | 0.0101392 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0048821 | GO:0048821 | erythrocyte development | 3/13 | 32/23276 | 7e-07 | 0.0001344 | 7.81e-05 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu04976 | mmu04976 | NA | 3/5 | 71/6698 | 0.0000112 | 0.0000450 | 0.0000118 |
| mmu04614 | mmu04614 | NA | 1/5 | 19/6698 | 0.0141073 | 0.0282146 | 0.0074249 |
NULL
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0050900 | GO:0050900 | leukocyte migration | 5/21 | 262/23276 | 0.0000031 | 0.0011583 | 0.0007223 |
| GO:0010743 | GO:0010743 | regulation of macrophage derived foam cell differentiation | 2/21 | 19/23276 | 0.0001313 | 0.0081437 | 0.0050780 |
| GO:0002446 | GO:0002446 | neutrophil mediated immunity | 2/21 | 24/23276 | 0.0002114 | 0.0096129 | 0.0059941 |
NULL
NULL
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu00290 | mmu00290 | NA | 1/4 | 11/6698 | 0.0065544 | 0.0491141 | 0.0140998 |
| mmu00770 | mmu00770 | NA | 1/4 | 15/6698 | 0.0089298 | 0.0491141 | 0.0140998 |
NULL
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu05145 | mmu05145 | NA | 2/3 | 128/6698 | 0.0010736 | 0.0257655 | 0.0079105 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0072283 | GO:0072283 | metanephric renal vesicle morphogenesis | 2/15 | 13/23276 | 0.0000301 | 0.0075758 | 0.0038011 |
| GO:0060343 | GO:0060343 | trabecula formation | 2/15 | 25/23276 | 0.0001153 | 0.0098772 | 0.0049558 |
(useful if replicating these results)
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel methods stats graphics grDevices utils
[8] datasets base
other attached packages:
[1] hexbin_1.27.1 vsn_3.40.0
[3] DEGreport_1.5.0 quantreg_5.24
[5] SparseM_1.7 RUVSeq_1.6.2
[7] EDASeq_2.6.2 ShortRead_1.30.0
[9] GenomicAlignments_1.8.0 Rsamtools_1.24.0
[11] Biostrings_2.40.0 XVector_0.12.0
[13] BiocParallel_1.6.2 dplyr_0.4.3
[15] cluster_2.0.4 org.Mm.eg.db_3.3.0
[17] AnnotationDbi_1.34.2 clusterProfiler_3.0.2
[19] DOSE_2.10.2 gridExtra_2.2.1
[21] logging_0.7-103 tximport_1.0.2
[23] DESeq2_1.12.2 SummarizedExperiment_1.2.2
[25] Biobase_2.32.0 GenomicRanges_1.24.0
[27] GenomeInfoDb_1.8.1 IRanges_2.6.0
[29] S4Vectors_0.10.0 BiocGenerics_0.18.0
[31] pheatmap_1.0.8 CHBUtils_0.1
[33] edgeR_3.14.0 limma_3.28.4
[35] gplots_3.0.1 reshape_0.8.5
[37] ggplot2_2.1.0 myRfunctions_0.1
[39] knitr_1.13 rmarkdown_0.9.6
[41] BiocInstaller_1.22.2
loaded via a namespace (and not attached):
[1] colorspace_1.2-6 hwriter_1.3.2 qvalue_2.4.2
[4] MatrixModels_0.4-1 topGO_2.24.0 affyio_1.42.0
[7] splines_3.3.0 R.methodsS3_1.7.1 GOSemSim_1.30.2
[10] DESeq_1.24.0 geneplotter_1.50.0 Formula_1.2-1
[13] Nozzle.R1_1.1-1 annotate_1.50.0 GO.db_3.3.0
[16] R.oo_1.20.0 graph_1.50.0 assertthat_0.1
[19] Matrix_1.2-6 formatR_1.4 acepack_1.3-3.3
[22] htmltools_0.3.5 tools_3.3.0 igraph_1.0.1
[25] coda_0.18-1 gtable_0.2.0 affy_1.50.0
[28] reshape2_1.4.1 DO.db_2.9 Rcpp_0.12.5
[31] preprocessCore_1.34.0 gdata_2.17.0 rtracklayer_1.32.0
[34] stringr_1.0.0 gtools_3.5.0 XML_3.98-1.4
[37] zlibbioc_1.18.0 MASS_7.3-45 scales_0.4.0
[40] aroma.light_3.2.0 RColorBrewer_1.1-2 yaml_2.1.13
[43] biomaRt_2.28.0 rpart_4.1-10 latticeExtra_0.6-28
[46] stringi_1.0-1 RSQLite_1.0.0 genefilter_1.54.2
[49] GenomicFeatures_1.24.2 caTools_1.17.1 chron_2.3-47
[52] matrixStats_0.50.2 bitops_1.0-6 evaluate_0.9
[55] lattice_0.20-33 GSEABase_1.34.0 plyr_1.8.3
[58] magrittr_1.5 R6_2.1.2 Hmisc_3.17-4
[61] DBI_0.4-1 foreign_0.8-66 survival_2.39-4
[64] RCurl_1.95-4.8 nnet_7.3-12 KernSmooth_2.23-15
[67] locfit_1.5-9.1 grid_3.3.0 data.table_1.9.6
[70] digest_0.6.9 xtable_1.8-2 tidyr_0.4.1
[73] R.utils_2.3.0 munsell_0.4.3